So I was troubleshooting the exact occurance of this problem, and it does occur or not occur whenever Photon is enabled/disabled, but the circumstances are very specific. In other words, the post content needs to be the following for the iframe attributes to be stripped:
A paragraph with a <a href="http://test.com/">link</a>.
<iframe src="http://www.youtube.com/embed/u9ie7k3orPc" height="480" width="640" frameborder="0"></iframe>
<iframe src="http://www.youtube.com/embed/ZFdqCjefcno" height="480" width="640" frameborder="0"></iframe>
This post was using nextgen gallery, which I don't think really matters to much, but when I remove the gallery snippet, the iframe attributes work fine, even with Photon enabled. Also, if I take out the link in the paragraph above, it works fine. So it's just like some weird off case in the above snippet. So not sure how this is effecting everything. If my issue is separate from Eminemdrdre00 I can start a new thread.
In other words, can you try an install with nextgen gallery (I'm using version 1.9.10) and the example I used above to see if you can reproduce.
It happens with different videos, not just the thing example above.